Searching journal content for articles similar to Hartmann et al. 23 (1): 181.

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  1. Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
    • Yidi Deng,
    • Jiadong Mao,
    • Jarny Choi,
    • and Kim-Anh Le Cao
    Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
    ...1Scalable cell-specific coexpression networks for granular regulatory 2 pattern discovery with NeighbourNet 3 Yidi Deng1,2, Jiadong Mao1,† & Jarny Choi3,† & Kim-Anh Lê Cao1,*,† 4 1Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, 5 3010, Australia 6...
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  2. Method: Multisample motif discovery and visualization for tandem repeats
    • Yaran Zhang,
    • Marc Hulsman,
    • Alex Salazar,
    • Niccolò Tesi,
    • Lydian Knoop,
    • Sven van der Lee,
    • Sanduni Wijesekera,
    • Jana Krizova,
    • Erik-Jan Kamsteeg,
    • and Henne Holstege
    Genome Res. April 2025 35: 850-862; Published in Advance November 13, 2024, doi:10.1101/gr.279278.124
    ...also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for the characterization and visualization of TRs based on a de novo k-mer approach for motif discovery. Comparative analysis against established...
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  3. Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
    • Yunxiao Ren,
    • Ming Hu,
    • Yang E. Li,
    • Andrew A. Pieper,
    • Jeffrey Cummings,
    • and Feixiong Cheng
    Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
    ...-regulators and cell type–specific regulatory landscapes of GWAS loci across AD progression by integrative analysis. (A) Top enriched TF motifs for each cell type. The color scale represents −log10 (adjusted P-value) of the normalized enrichment score. (B) Tn5 bias-corrected TF footprinting for SPI1. (C) Positive TF...
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  4. Method: Iterative improvement of deep learning models using synthetic regulatory genomics
    • André M. Ribeiro-dos-Santos and
    • Matthew T. Maurano
    Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
    ...not accurately reflect the mESC trans-regulatory environment. These SynHPRT1R false positives might be related to sequence CpG content, because they were absent in SynHPRT1RnoCpG. These results reinforce model limitations when assessing novel synthetic sequences.View larger version: In this window In a new...
  5. Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
    • Qinhu Zhang,
    • Siguo Wang,
    • Zhipeng Li,
    • Wenzheng Bao,
    • Wenjian Liu,
    • and De-Shuang Huang
    Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
    ..., we find a pattern in true positives (TPs) that the regulatory effect of cCREs on genes decreases with distance. Inspired by the pattern, we design two methods to enhance the ability to capture distal cCRE–gene interactions by incorporating chromatin loops into the ScPGE model. Furthermore, Sc...
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  6. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M Riley,
    • Randa Elsayed,
    • Mark D Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C Nelson
    Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...There are well-characterised examples of “suboptimisation” of TFBSs within developmental 380 CRMs, where low affinity TFBSs tune target gene expression preventing deleterious ectopic 381 or overexpression (Farley et al. 2015; Farley et al. 2016). However, position frequency 382 matrices used for most motif...
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  7. Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
    • Taylor Anglen,
    • Irene M. Kaplow,
    • Baekgyu Choi,
    • Enya Dewars,
    • Robin M. Perelli,
    • Kevin T. Hagy,
    • Duc Tran,
    • Megan E. Ramaker,
    • Svati H. Shah,
    • Inkyung Jung,
    • Andrew P. Landstrom,
    • Ravi Karra,
    • Yarui Diao,
    • and Charles A. Gersbach
    Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
    ...rounds of analysis were conducted. First, motif discovery using the MEME suite was performed on all differentially accessible peaks (Padj < 0.05) to identify general trends and TFs associated with peaks showing decreased accessibility, increased accessibility, and focused analysis on R3 (Supplemental...
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  8. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...used to map 51 open chromatin and histone modifications across the , enabling the identification of 52 putative regulatory elements. While these assays are powerful, they have limitations, 53 including the potential for false positives (regions that are accessible but not functionally 54 active...
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  9. Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
    • Wenhao Zhang,
    • Lan Cao,
    • Xiaoxuan Gu,
    • Yongyu Long,
    • and Ying Wang
    Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
    ...to recover GRNs by integrating multi-omics data. scAI (Jin et al. 2020) combines sparse epigenomic signals with transcriptomic information by matrix factorization, enabling the discovery of regulatory relationships within a unified low-dimensional representation of cells. Similarly, scREG (Duren et al. 2022...
  10. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...(Fig. 3H). Considering that the differential usage of PASs might change the number of RBP binding sites, we scanned the CD47 differential 3′ UTR using RBP motif position weight matrices. This analysis revealed that most RBP binding motifs within this region corresponded to ELAVL1 and ELAVL2 (Fig. 3I...
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